Entering edit mode
7.2 years ago
vassialkalive23
•
0
How to output VarsScan variant calling results in a .tab or txt/csv file? I run code line
samtools mpileup -f H37Rv_reference.fa ls_sorted.bam | java -jar VarScan.jar pileup2snp --output-file varscan_results.tab
but there is not saved output, it says:
1115568 bases in pileup file 979731 met minimum coverage of 8x 7055 SNPs predicted
how to save results in a file?
You are using mpileup with pileup2snp, did you try using with mpileup2snp?